We show that the topography of Madagascar is essential to adequately simulate the atmospheric circulation and rainfall over southern Africa and the neighboring southwest Indian Ocean. By conducting a set of numerical experiments, we evaluate the role of Madagascar and its topography in shaping the regional climate. The underlying mechanism through which reduced topography over Madagascar leads to more moisture transported from the Indian Ocean to the African mainland is analyzed. The results also help explain the often observed dipole rainfall anomaly between Madagascar and the mainland and the tendencies for climate models to inadequately represent a realistic mean rainfall pattern over the region. Our results may therefore help in improving the accuracy of models used for seasonal outlooks and climate change projections over Africa.